Human activity in the last century has led to a substantial increase in nitrogen (N) emissions and deposition (Galloway et al. 2003). Because of past, and, in some regions, continuing increases in emissions (Lehmann et al. 2005, Nilles and Conley 2001), this N deposition has reached a level that has caused or is likely to cause alterations and damage in many ecosystems across the United States. In some ecoregions, the impact of N deposition has been severe and has changed the biotic community structure and composition of ecosystems. In the Mediterranean California ecoregion, for example (see Chapter 13), replacement of native by exotic invasive vegetation is accelerated because exotic species are often more productive under elevated N deposition than native species in some California grasslands, coastal sage scrub, and desert scrub (Fenn et al. 2010, Rao and Allen 2010, Rao et al. 2010, Weiss 1999, Yoshida and Allen 2004). Such shifts in plant community composition and species richness can have consequences beyond changes in ecosystem structure: shifts may lead to overall losses in biodiversity and further impair particular threatened or endangered species (Stevens et al. 2004). Th e extirpation of the endangered checkerspot butterfl y (Euphydryas editha bayensis), because the host plant for the larval stage disappears in N-enriched ecosystems (Fenn et al. 2010, Weiss 1999), is just one example of the detrimental impacts of elevated N deposition.